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Maybe possibly considering an LS1 swap this winter over the previously planned Gen1 I was building. The concern I have is I have already purchased a BTO 2004r and all the installation accessories. I know there are adapters for the LS to this trans, but does the back of the LS motor fall in the right place to make the trans install otherwise the same as a gen1? Is it worth it overall to try and use the 2004r or just sell and get an entire ls drivetrain? What pros/cons would either choice have?
I'd suggest reading through the sticky at the top of the page. There is probably someone who has used that combination. It will take a while to get through the whole thread but you will also get a better idea of what is involved in a LS engine swap.
You might try sending a PM to Speed Hound. He sells adapter plates and headers for LS1 conversions and he might know the dimensions that will work. There is a lot to absorb in understanding merging 2000's technology with 1960's technology. The wiring of the LS engine really isn't bad. The fuel system has to be re-designed but there are a lot of folks here who have done it successfully, and the design will vary depending on your fuel tank. Best thing to do is just jump into the pool. Search the sticky for info and ask questions there when you don't understand something.